Friday, 27 April 2018

Finding Texas carbons and other unusual valencies

So, having disposed of the phrase "invalid molecule" in the previous post, let's find some :-). Step one is to define what I mean by "invalid molecule": I'm going to use this to mean any molecule that contains an atom that is not on a list of common charge states and valencies. Rather conveniently, I have a table to hand provided by Daniel Lowe which I can use for this purpose. If an element is not in the table, it's fine; but if it is, then it has to be in one of the listed charge states and valencies.

The code is shown below, but first, the results for ChEMBL 23 (you can copy the whole lot and paste into John Mayfield's CDKdepict to view). There are a couple of Texas carbons, oxygen radicals, and TEMPO-like nitrogens that should be neutral. That's not to say that everything found is dodgy - nitrogen monoxide is rumoured to be stable, for example - but they are definitely unusual and warrant further inspection.